The elongating ribosome essentially carries out the same step, peptide bond synthesis, over and over until a termination codon is reached. Several sites exist for binding aminoacyl‐tRNAs on each ribosome. For the purposes of this book, however, only two are of importance. The A (acceptor) site is where the incoming aminoacyl‐tRNA is bound to the ribosome. The initial step of decoding by codon‐anticodon base‐pairing occurs here. The P (peptidyl) site is where the peptidyl‐ (or initiator fmet‐) tRNA is bound. Peptide bond synthesis involves the transfer of the peptide or fmet from the P site tRNA onto the free amino group of the A site aminoacyl‐tRNA. Note how this means that the protein is synthesized in the amino‐ to the carboxyl‐ direction (N‐C). After the peptide bond is formed, the ribosome translocates, moving the new peptidyl‐tRNA from the A site to the P site, and the cycle begins again. See Figure 1 .
The elongation process is carried out with the assistance of elongation factors that use GTP to deliver the new aminoacyl‐tRNA to the ribosomal A site. EF‐Tu (u stands for “unstable”) binds to amino‐acyl‐tRNA and GTP. After it is bound to the ribosome, EF‐Tu hydrolyzes the GTP to GDP and inorganic phosphate. A second factor, EF‐Ts (s stands for “stable”) binds to the complex of GDP and Ts, causing GDP to be released from the factor so it can be replaced by GTP. Ts is therefore a guanine nucleotide exchange factor; it is displaced from Tu when GTP binds. Tu is now available for amino‐acyl‐tRNA binding, as shown in Figure 2 .
The 23S rRNA of the large ribosomal subunit catalyze the actual process of peptide bond formation. The synthesis of the peptide bond requires no energy input; it occurs because the aminoacyl bond of the tRNA at the P site is itself a “high energy” bond, with a free energy of hydrolysis essentially equal to that of an ATP phosphate. The peptide bond is more stable to hydrolysis, meaning that energy flows “downhill” during the process just as in the formation of amides from active esters in other organic reactions.
Translocation, however, requires the input of energy (again, in the form of GTP) with the participation of the elongation factor EF‐G. The translocation reaction moves the peptidyl‐tRNA from the A‐site to the P‐site. The uncharged tRNA is removed from the P‐site (it remains bound at an Exit or E‐site for another cycle of elongation), while the ribosome and mRNA move relative to each other. This is shown in Figure 3
The A‐site is free to accept the next aminoacyl‐tRNA bound to elongation factor T u. The growing peptide chain folds while still on the ribosome. As the ribosome moves down the mRNA chain, the initiation region (RBS) of the mRNA becomes available for reinitiation. This leads to the formation of a single mRNA with many ribosomes bound to it, called a polysome,as shown in Figure 4.